Sample testing methods with automated cleaning

ABSTRACT

A sample testing system includes a test receptacle support structure, an optical element positioned for transmitting electromagnetic radiation emitted or reflected by a sample disposed in a test receptacle supported by the test receptacle support structure, a cleaning member, and an automated transport arm configured to (i) detachably couple the cleaning member, (ii) move the detachably-coupled cleaning member into a position proximate to and/or contacting the optical element, and (iii) decouple the cleaning member.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/094,227, filed Apr. 8, 2016, now U.S. Pat. No. 9,810,622, whichclaims the benefit of U.S. Provisional Application No. 62/145,247, filedApr. 9, 2015, the contents of each are hereby incorporated by referenceherein.

FIELD

Embodiments of the present disclosure relate generally to systems,apparatuses, devices, and methods for performing automated biochemicalassays, including nucleic acid-based assays, using optical elements,such as optical fibers, to transmit electromagnetic radiation reflectedand/or emitted by samples contained in test receptacles, includingautomated cleaning of such optical elements and/or other systemcomponents.

BACKGROUND

Exemplary systems, apparatuses and methods for performing automatedbiochemical assays employing optical fibers to transmit electromagneticradiation reflected and/or emitted by samples contained in testreceptacles, are disclosed and described, by way of non-limitingexamples, in each of U.S. Published Patent Application No. US2014-0263984 A1, entitled “Indexing Signal Detection Module”;International Application No. WO 2014/153193 A2, entitled “DiagnosticSystems and Methods”; U.S. Published Patent Application No. No. US2014-0263153 A1, entitled “Interlocking Cap and Receptacle for AutomatedProcesses”; U.S. Published Patent Application No. US 2014-0038192 A1,entitled “System, Method and Apparatus for Automated Incubation”; andU.S. application Ser. No. 14/213,900, entitled “Method for Analyzing aPlurality of Samples,” and filed on Mar. 14, 2014. The full contents ofeach of the foregoing applications are hereby incorporated by referenceherein in their entirety.

As disclosed and described in U.S. Published Patent Application No. US2014/0263984 A1, a “thermocycler” of an exemplary system used forperforming automated fiber optic interrogation (testing) of a sample,such as a biological sample, includes a plurality of test receptacleholders (e.g., 12), each holder having a plurality of (e.g., 5) testreceptacle wells. Each test receptacle well has an open bottom end, andis configured to have a test receptacle seated therein in a stablemanner By this arrangement, optical interrogation of a sample containedin a test receptacle seated in the test receptacle well may be performedusing light transmitted and/or received through an axial-facing distalend of an optical fiber positioned proximate the open bottom of therespective test receptacle well.

For the test results to be reliable, it is critical that the opticalpathway extending between, and including, the end surfaces of therespective optical fiber and test receptacle be free and clear of anydebris, such as dust, fibers, hair and/or other particulate materials,that may interfere with the optical interrogation process. Debris can beespecially problematic when the test receptacle holders are open to theatmosphere (i.e., without any cover or lid) in order to allow for easyinsertion and extraction of the test receptacles into and out of thetest receptacle wells. Debris may exhibit autofluorescence, i.e., inwhich the debris material naturally fluoresces, or may benon-fluorescent. While debris that fluoresces is generally easy todetect, debris that does not fluoresce can be difficult to detect. As aresult, non-fluorescing debris can interfere with the passage of lightwithout being detected and, consequently, lead to false or misleadingtest results.

As such, upon detection of any debris on or over the end of an opticalfiber that may be interfering with a light signal path, the respectivetest receptacle well(s) and optical fiber end are not able to be used toperform further testing of sample test receptacles until they aremanually cleaned, e.g., using a cotton swab or compressed air (similarto cleaning a keyboard). Furthermore, because some types of interferingdebris are not readily detectable, the axial-facing ends of the opticalfibers must be periodically cleaned, generally during routine servicingby a field service technician, to ensure that non-detected debris doesnot have an adverse effect on the sample testing. The frequency ofregular cleaning can be expensive both in terms of the cleaning expense,and in terms of the lost time for testing while the system is shut-downfor cleaning. Moreover, in the event immediate manual cleaning ofdetected debris is not performed, the respective optical fiber and/ortest receptacle well are no longer available for reliable testing in themeantime, and their use must be disabled, thereby reducing thethroughput of the system.

Other components of the sample testing systems may also require periodicmanual cleaning and/or sterilization. For example, test receptacle wellsmay be exposed to sample material or reagents on the outer surfaces ofreceptacles, flakes of plastic, hair and/or environmental particles orcontaminates, and may also require periodic manual cleaning and/orsterilization to avoid cross-contamination between samples or otherproblems that may arise as a result of such exposure.

None of the references described, referred to, and/or incorporated byreference herein are admitted to be prior art.

SUMMARY

In accordance with the disclosed embodiments herein, an exemplary sampletesting system includes a test receptacle support structure; an opticalelement positioned for transmitting electromagnetic radiation emitted orreflected by a sample disposed in a test receptacle supported by thetest receptacle support structure; a cleaning member; and an automatedtransport arm configured to detachably couple with the cleaning member,where the automated arm is further configured to move adetachably-coupled cleaning member into a position proximate to and/orcontacting the optical element, and (thereafter) decouple the cleaningmember. The system preferably includes a controller that controlsoperation of the automated transport arm for causing the automatedtransport arm to detachably couple with the cleaning member, and to movethe detachably-coupled cleaning member into a position proximate toand/or contacting the optical element based upon one or both of a (i)predetermined cleaning schedule, and (ii) sensed presence ofparticulates and/or other materials disposed on or over the opticalelement. The automated transport arm may be an articulating arm,although this is not necessary for practicing the disclosed embodiments.In some embodiments, the automated transport arm is configured todeposit the decoupled cleaning member into a waste output. In someembodiments, the sample testing system is provided with one or morecleaning member holders, each configured to hold one or more cleaningmembers, where the automated transport arm may be configured toselectively deposit the decoupled cleaning member into the same or adifferent cleaning member holder from which the decoupled cleaningmember was removed.

The cleaning member of the exemplary embodiment includes a proximalcoupling element joined to a distal cleaning element, where the couplingelement has a proximal end portion configured to releasably mate with adistal working end portion of the automated transport arm. The couplingelement and the cleaning element may be separately molded components, inwhich a distal portion of the coupling element forms, by way ofnon-limiting examples, an interference fit or a frictional fit with aproximal portion of the cleaning element in order to subsequently jointhe elements together. Alternatively, the coupling element and thecleaning element may be co-molded as a single component. The automatedtransport arm is preferably configured to move the detachably-coupledcleaning member into a position such that the cleaning element isinserted into a test receptacle well of the test receptacle supportstructure, and where the cleaning element is dimensioned such that anouter surface of the cleaning element conforms to an interior surface ofthe test receptacle well. By way of non-limiting example, the outersurface of the cleaning element and the interior surface of the testreceptacle well may have complementary, frustoconical shapes. Thecleaning element preferably cleans, decontaminates and/or sterilizes theinterior surface of the test receptacle well when inserted therein. Inone embodiment, the test receptacle well has an open bottom, and theoptical element is an optical fiber having an end positioned proximateto the open bottom of the test receptacle well, where the cleaningelement cleans, decontaminates and/or sterilizes the end of the opticalfiber when inserted into the test receptacle well.

In exemplary embodiments, the cleaning element may be made out of anadhesive material, such as (without limitation) silicone, platinum curedsilicone, thermoplastic polyurethane, thermoplastic elastomer,thermoplastic rubber, or a gel. Additionally or alternatively, thecleaning element may be made out of a material that generates a staticattraction to particulates and/or other materials that can interferewith the transmission by the optical element of electromagneticradiation emitted or reflected by the sample, such as (withoutlimitation) silicon, polyvinyl chloride, polypropylene, polyethylene,polyurethane, polyester or polystyrene. In other embodiments, thecleaning element may be made out of an absorbent material capable ofretaining and applying a fluid substance, such as (without limitation)isopropyl alcohol, ethyl alcohol, diluted hydrochloric acid, oxalicacid, diluted sodium hydroxide and diluted sodium hypochlorite.

In one exemplary embodiment, the sample testing system includes one ormore test receptacle holders, each test receptacle holder comprising aplurality of test receptacle wells, each test receptacle well having anopen bottom end and configured to have a test receptacle seated therein.A plurality of optical fibers are arranged with respect to the one ormore test receptacle holders, such that an end of a respective opticalfiber is (or may be) positioned proximate to the open bottom end of eachtest receptacle well to allow for transmission of electromagneticradiation emitted or reflected by a sample contained in a testreceptacle seated in the test receptacle well. The system of thisembodiment further includes a cleaning member holder comprising aplurality of cleaning member wells, each of a plurality of the cleaningmember wells configured for having a cleaning member seated therein. Thesystem further includes an automated transport arm configured to (i)detachably couple a cleaning member located in one of the cleaningmember wells, (ii) remove the detachably-coupled cleaning member fromthe respective cleaning member well, (iii) insert a distal portion ofthe detachably-coupled cleaning member into one of the test receptaclewells, such that a distal end of the cleaning member is positionedproximate to or contacting the end of the optical fiber positionedproximate to the open bottom end of the respective test receptacle well,(iv) remove the detachably-coupled cleaning member from the respectivetest receptacle, and (v) decouple the cleaning member.

The automated transport arm is preferably configured to selectivelydeposit the decoupled cleaning member into the same or a differentcleaning member well from which the decoupled cleaning member wasremoved. Alternatively and/or additionally, the automated transport armis configured to selectively deposit the decoupled cleaning member intoa waste output. The system preferably includes a controller thatcontrols operation of the automated transport arm for causing theautomated transport arm to detachably couple with a cleaning memberlocated in a respective cleaning member well, and to move thedetachably-coupled cleaning member into a position proximate to and/orcontacting the one or more optical fiber ends based upon one or both ofa (i) predetermined cleaning schedule, and (ii) sensed presence ofparticulates and/or other materials disposed on or over the opticalfiber ends. Depending on the relative position of the optical fiber, thedistal portion of the cleaning member of this embodiment may bedimensioned to extend to and/or through the open bottom end of therespective test receptacle well in order for the distal tip of thecleaning member to be located proximate to or in contact with the end ofthe respective optical fiber. The cleaning element is preferablydimensioned such that an outer surface of the cleaning element conformsto an interior surface of the test receptacle well, such that thecleaning element cleans, decontaminates and/or sterilizes one or both of(i) the interior surface of the test receptacle well, and (ii) the endof the respective optical fiber, when the cleaning element is insertedinto the test receptacle well.

In accordance with another aspect of the disclosed embodiments, acleaning member is provided for use in an automated sample testingsystem, the cleaning member including a proximal coupling element, and adistal cleaning element, the coupling element having a proximal endportion configured to releasably mate (e.g., by forming a frictionalfit) with the working end of an automated transport arm. The couplingelement and the cleaning element may be separately molded components, inwhich a distal portion of the coupling element forms, by way ofnon-limiting examples, an interference fit or a frictional fit with aproximal portion of the cleaning element in order to subsequently jointhe elements together. Alternatively, the coupling element and thecleaning element may be co-molded as a single component. The cleaningelement is preferably dimensioned such that an outer surface of thecleaning element conforms to an interior surface of a test receptaclewell of the sample testing system. By way of non-limiting example, theouter surface of the cleaning element and the interior surface of thetest receptacle well may have complementary frustoconical shapes. Thecleaning element may be made out of an adhesive material, such as(without limitation) silicone, platinum cured silicone, thermoplasticpolyurethane, thermoplastic elastomer, thermoplastic rubber, or a gel.Additionally or alternatively, the cleaning element may be made out of amaterial that generates a static attraction to particulates and/or othermaterials that can interfere with the transmission by the opticalelement of electromagnetic radiation emitted or reflected by the sample,such as (without limitation) silicon, polyvinyl chloride, polypropylene,polyethylene, polyurethane, polyester or polystyrene. In otherembodiments, the cleaning element may be made out of an absorbentmaterial capable of retaining and applying a fluid substance, such as(without limitation) isopropyl alcohol, ethyl alcohol, dilutedhydrochloric acid, oxalic acid, diluted sodium hydroxide and dilutedsodium hypochlorite.

In accordance with further disclosed embodiments, methods for operatinga sample testing system include using an automated transport arm to (i)detachably couple a cleaning member to a working end of the transportarm; (ii) move the detachably-coupled cleaning member into a positionproximate to and/or contacting an optical element, such that thecleaning member thereby cleans and/or sterilizes the optical element;and (iii) decouple the cleaning member from the working end of thetransport arm. In an exemplary embodiment, the test system includes acleaning member holder having a plurality of cleaning memberreceptacles, the cleaning member being one of a plurality of cleaningmembers held in respective cleaning member receptacles of the cleaningmember holder, where the automated transport arm detachably couples thecleaning member while the cleaning member is held by the respectivecleaning member receptacle.

In an exemplary method, the cleaning member has a proximal couplingelement and a distal cleaning element, where the automated armdetachably couples the cleaning member to the working end portion of thetransport arm by detachably coupling a proximal end portion of thecoupling element to the working end of the transport arm, and insertinga distal end connector of the coupling element into a recessed proximalportion of the cleaning element to thereby attach (e.g., by aninterference or frictional fit) the cleaning element to the couplingelement. In some such embodiments, the system includes a cleaningelement holder having a plurality of cleaning element receptacles, thecleaning element being one of a plurality of cleaning elements held inrespective cleaning element receptacles of the cleaning element holder.In particular, the automated transport arm inserts the distal endconnector of the coupling element into the recessed proximal portion ofthe cleaning element while the cleaning element is held in therespective cleaning element receptacle. In such embodiments, thecleaning elements may be substantially environmentally sealed in theirrespective cleaning element receptacles by a frangible sealing memberthat is pierced when the distal end connector of the coupling element isinserted into the recessed proximal portion of the respective cleaningelement.

Such method(s) may further include using the automated transport arm tomove the detachably-coupled cleaning member into a position such thatthe cleaning element is inserted into a test receptacle well of the testreceptacle support structure, wherein the cleaning element isdimensioned such that an outer surface of the cleaning element conformsto an interior surface of the test receptacle well, where the cleaningelement cleans, decontaminates and/or sterilizes the interior surface ofthe test receptacle well when inserted therein. In an exemplaryembodiment, the test receptacle well has an open bottom, and the opticalelement comprising an optical fiber having an end positioned proximateto the open bottom of the test receptacle well, where the cleaningelement cleans, decontaminates and/or sterilizes the end of the opticalfiber when inserted into the test receptacle well.

In one embodiment, the detachably-coupled cleaning member comprises afirst cleaning member, and the cleaning element of the first cleaningmember comprises a first cleaning element, the method furthercomprising, after decoupling the first cleaning member from the workingend of the automated transport arm, using the automated transport arm todetachably couple a second cleaning member to the working end of theautomated transport arm, the second cleaning member comprising a secondcleaning element; and move the detachably-coupled second cleaning memberinto a position such that the second cleaning element is inserted intothe same test receptacle well of the test receptacle support structure.In such embodiment, the first cleaning element may be made of adifferent material (e.g., an adhesive material) than the second cleaningelement (e.g., made of an absorbing material and carrying a cleaningand/or sterilizing fluid).

In accordance with the disclosed methods, a controller may controloperation of the automated transport arm for causing the automatedtransport arm to detachably couple with a respective cleaning member,and to move the respective detachably-coupled cleaning member into aposition proximate to and/or contacting the optical element based uponone or both of a (i) predetermined cleaning schedule, and (ii) sensedpresence of particulates and/or other materials disposed on or over theoptical element. The controller may further cause the automatedtransport arm to deposit respective decoupled cleaning members into asystem waste output or a designated used cleaning member holder.

Other and further aspects and features of embodiments will becomeapparent from the ensuing detailed description in view of theaccompanying figures.

BRIEF DESCRIPTION OF THE DRAWINGS

The drawings illustrate the design and utility of the disclosedembodiments, in which similar elements are referred to by commonreference numerals. These drawings are not necessarily drawn to scale.In order to better appreciate how the above-recited and other advantagesand objects are obtained, a more particular description of theembodiments will be rendered, which are illustrated in the accompanyingdrawings. These drawings depict only typical embodiments and are nottherefore to be considered limiting of its scope.

FIG. 1 is an exploded perspective view of an exemplary cleaning memberconstructed according to embodiments disclosed herein, and furtherillustrating the working end (“disposable tip interface”) of anautomated transport mechanism that detachably couples with a proximalportion of the cleaning member.

FIG. 2 is a perspective side view of the cleaning member of FIG. 1, whenassembled or as molded.

FIG. 3 is a cross-sectional side view of the fully assembled or moldedcleaning member of FIG. 1, showing co-molding or an interference fitthat joins a proximal coupling element with a distal cleaning element ofthe cleaning member.

FIGS. 4 and 5 are respective cross-sectional side elevation andcross-sectional side perspective views of the disposable tip interfaceof FIG. 1, inserting a detachably-coupled cleaning member into a testreceptacle well of a test receptacle holder, wherein a distal tip of thecleaning member contacts an upward, axial facing end of an optical fiberpositioned proximate to an open bottom portion of the test receptaclewell.

FIG. 6 is a top plan view of an exemplary sample processing instrumentdeck of an automated sample testing system.

FIG. 7 is a perspective view of an automated transport gantry for usewith the sample processing instrument deck of FIG. 6.

FIG. 8 is a perspective view of a transport arm of the transport gantryof FIG. 7.

FIG. 9 is a perspective view of an exemplary cleaning member storagetray constructed according to embodiments disclosed herein, and furtherillustrating an exploded perspective view of an exemplary cleaningmember seated in a corner cleaning member well of the storage tray.

FIG. 10 is a top view of the cleaning member storage tray of FIG. 9,including the seated cleaning member.

FIG. 10A is a cross-sectional view taken along lines A-A in FIG. 10.

FIG. 10B is a cross-sectional view taken along lines B-B in FIG. 10.

FIGS. 11A and 11B are respective side views of the cleaning memberstorage tray of FIG. 9.

FIG. 12 is a bottom view of the cleaning member storage tray of FIG. 9.

FIG. 13 is a perspective view of an exemplary cleaning member storagetray holder constructed according to embodiments disclosed herein.

FIG. 14 is a perspective view of a portion of a sample processinginstrument deck, with the cleaning member storage tray holder of FIG. 13installed thereon.

DETAILED DESCRIPTION

Before the present systems, methods, and apparatuses are described, itis to be understood that this disclosure is not limited to particularmethods, components and materials described, as such methods, componentsand materials may vary. It is also to be understood that the terminologyused herein is for purposes of describing particular embodiments only,and is not intended to be limiting, since the scope of the presentdisclosure will be limited only in the appended claims.

Various components and sub-assemblies of embodiments of exemplary sampletesting systems will now be described in conjunction with theaccompanying figures. The figures are not necessarily drawn to scale,the relative scale of select elements may have been exaggerated forclarity, and elements of similar structures or functions are representedby like reference numerals throughout the figures. It should also beunderstood that the figures are only intended to facilitate thedescription of the embodiments, and are not intended as an exhaustivedescription of the disclosed embodiments or as a limitation on the scopeof the disclosure, which is defined only by the appended claims andtheir equivalents. In addition, an illustrated embodiment needs not haveall the aspects or advantages shown. An aspect or an advantage describedin conjunction with a particular embodiment is not necessarily limitedto that embodiment and can be practiced in any other embodiments even ifnot so illustrated.

For the following defined terms, these definitions shall be applied,unless a different definition is given in the claims or elsewhere inthis specification.

All numeric values are herein assumed to be modified by the term“about,” whether or not explicitly indicated. The term “about” generallyrefers to a range of numbers that one of skilled in the art wouldconsider equivalent to the recited value (i.e., having the same functionor result). In many instances, the term “about” may include numbers thatare rounded to the nearest significant figure. The recitation ofnumerical ranges by endpoints includes all numbers within that range(e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, and 5).

As used in this specification and the appended claims, the singularforms “a”, “an”, and “the” include plural referents unless the contentclearly dictates otherwise. Thus, for example, references to “themethod” includes one or more methods, and/or steps of the type describedherein, which will become apparent to those persons skilled in the artupon reading this disclosure and so forth. As used in this specificationand the appended claims, the term “or” is generally employed in itssense including “and/or” unless the content clearly dictates otherwise.

The term “comprising,” which is used interchangeably with “including,”“containing,” “having,” or “characterized by,” is inclusive oropen-ended language and does not preclude or exclude possible additionalelements or acts. The phrase “consisting of” excludes any element, step,or ingredient not specified in the claim. The present disclosurecontemplates exemplary embodiments of an apparatus and methods of usethereof corresponding to the scope of each of these phrases. Thus, asystem, device or method comprising recited elements or stepscontemplates particular embodiments in which the system, device ormethod consists essentially of or consists of those elements or steps.

FIGS. 1-3 depict an exemplary cleaning member 100 for use in a sampletesting system, according to embodiments disclosed herein. The cleaningmember 100 includes a distal cleaning element 102 and a proximalcoupling element 104. As described below in greater detail, therespective cleaning and coupling elements 102 and 104 may bemanufactured (e.g., molded) as separate components as depicted in FIG.1, and subsequently joined together, as depicted in FIGS. 2 and 3.Towards this end, the coupling element 104 has a distally projectingextension member 105 including a plurality of radially extendingprotuberances 106. The extension member 105 and protuberances 106 aredimensioned to form an interference fit with a complementary-dimensionedinterior cavity 107 of the cleaning element 102, which is accessedthrough a proximal end opening 108 thereof. The material(s) used to makethe cleaning element 102 and/or coupling element 104 are thus preferablysufficiently compliant relative to each other so that the couplingelement 104 is fixedly-joined to the cleaning element 102 by insertingthe extension member 105 through opening 108, until the extension member105 (including the protuberances 106) makes a “snap-fit” connectionwithin the cavity 107. A radially outward ring 110 disposed on thecoupling element 104 butts against a rim 109 surrounding the proximalopening 108 to prevent over-insertion of the extension member 105 intocavity 107. It will be appreciated that alternative attachmentmechanisms and configurations may be used to join together the cleaningand coupling elements 102 and 104, such as a frictional fit, a weld, oran adhesive.

The respective cleaning and coupling elements 102 and 104 may be joinedtogether prior to providing the (assembled) cleaning member 100 for usein a sample testing system, or alternatively the cleaning and couplingelements 102 and 104 may be provided as separate components that arejoined together by the system at the time of using the cleaning member100. By way of example, a system testing system may include a firststructure that holds one or more cleaning elements 102, and a secondstructure that supports or holds one or more coupling elements 104. Atthe time of use, a working end of an automated transport arm engages(i.e., detachably couples with) a coupling element 104 held in thesecond support structure, and transports the detachably-coupled couplingelement 104 to a location proximate a cleaning element 102 held in thefirst support structure. The automated arm maneuvers the couplingelement 104 to insert the extension member 105 thereof through the openproximal end 108 and interior cavity 107, respectively, of the cleaningelement 102, to thereby form an interference fit to join the couplingelement 104 to the respective cleaning element 102. The fully assembledcleaning member 100 is then ready to use and already coupled to theautomated transport arm. The cleaning elements 102 in the foregoingexample may be environmentally sealed prior to use, e.g., inindividually sealed receptacles, or in a sealed tray, in which afrangible member forming the respective seal is penetrated by theextension member 105, as the coupling element 104 engages the cleaningelement 102.

Alternatively, the cleaning member 100 may be manufactured as anintegral unit, e.g., in which the respective cleaning and couplingelements 102 and 104 are formed in their joined configuration using aco-molding process. In such embodiments, such as the below-describedembodiments shown in FIGS. 9-14, it may still be desirable toenvironmentally seal the cleaning member(s) 100 prior to use, e.g., inindividually sealed receptacles, or in a sealed tray, in which afrangible member forming the respective seal is penetrated by theworking end of the automated transport arm as it engages the proximalend of the coupling element 104 of the cleaning member 100.

By way of illustration and with specific reference to FIG. 1, a proximalbody portion 118 of the coupling element 104 forms an elongated,funnel-shaped interior recess 117 that is accessed through the openproximal end 112 of the coupling element 104. The open end 112 of thecoupling element 104 is bordered by a rim 125 having an axially facingsurface. The recess 117 (best seen in FIGS. 3, 4 and 5) is dimensionedto receive and releasably engage (mate) with the working end(“disposable tip interface” or “DiTi”) 302 of an automated transport arm300. In particular, radially enlarged protrusions 304 and 306 disposedon the DiTi 302 form a frictional fit with an interior surface 113 ofthe interior recess 117 to thereby detachably-couple the DiTi 302 withthe coupling element 104 when the DiTi 302 is inserted through the openend 112 thereof. The detachably-coupled components 102 and 104 maythereafter be de-coupled (i.e., detached) by action of a sleeve 308 thatmoves relative to the DiTi 302 by one or both of advancement of thesleeve 308 over the DiTi 302, or by withdrawal of the DiTi 302 into thesleeve 308, until a distal end 309 of the sleeve 308 contacts andengages the proximal rim 125 of the coupling element 104 to dislodge thecoupling element 104 from the DiTi 302.

As best seen in FIG. 3, a plurality of longitudinally oriented linearribs 126 are formed on the interior surface 113 of the coupling element104. While there are three linear ribs 126 depicted in the illustratedembodiments, alternative embodiments may have a fewer (i.e., 1 or 2) orgreater (i.e., 4 or more) amount of linear ribs 126 on the interiorsurface 113. In further alternative embodiments, no linear ribs 126 areprovided on the interior surface 113, and the ribs 126 in the depictedembodiments should be considered optional. In embodiments having atleast two linear ribs 126, the ribs 126 are preferably spacedsubstantially equal distances apart from one another on the interiorsurface 113. Accordingly, in the illustrated embodiments, the three ribs126 are spaced approximately one hundred twenty degrees apart from eachother on the interior surface 113. The ribs 126 each protrude inwardinto recess 117 along their length, thereby decreasing the inner fitmentdiameter of the recess 117 to facilitate engagement of the DiTiprotuberances 304 and 306 to the coupling element 104. The ribs 126 maybe beveled at an upper, or proximal, end thereof or otherwise preferablydimensioned to at least partially deform as the DiTi protuberances 304and 306 are inserted into the recess 117. In some embodiments, theamount of protrusion of the ribs 126 may gradually increase in size asthe respective ribs approach the bottom of the recess 117 within thecoupling member 104. In the illustrated embodiments, the thickness ofthe ribs is increased at a radial-inward apex 138 within the recess 117,and thereafter reduced, wherein a bottom portion 139 of each rib 126 isrecessed to accommodate the frictional engaging protuberance 304 on theDiTi 302. Alternatively, or in addition thereto, in certain embodiments,the linear ribs 126 may gradually increase in overall thickness as theyapproach the bottom of the recess. Thus, a gradual increase in thicknessand/or radial geometry is contemplated for the gradual tapering of theone or more linear ribs 126, which additionally serves to center theDiTi 302 as it is inserted through open end 112 of the coupling element104, and into recess 117.

One or more longitudinal indentations, or recesses 124, are disposed on,and extend along at least part of the length of, the exterior surface118 of the coupling element 104. The recesses 124 may be formed in anyshape such as, for example, concave, notched, squared, etc. In variousembodiments, the length of each of the one or more recesses 124 isaligned with (i.e., in direct opposition), and is approximately the samelength as, a corresponding linear rib 560 disposed on the interiorsurface 113. Thus, the illustrated embodiment has three exterior linearrecesses for a one-to-one relationship with the respective three linearribs 126 on the interior surface 113. The coupling of an interiorsurface linear rib 126 with an exterior surface recess 124 enhances thepredictability of the frictional attachment of the coupling element 104with the DiTi 302 of the automated transport arm 300. In particular, asthe DiTi 302 of the transport arm 300 is lowered into the recess 117 ofthe coupling element 104, the distal end protuberances 304 and 306 ofthe DiTi 302 contact and press against the linear ribs 126, therebycausing the coupling element 104, and in particular the one or morerecesses 124, to flex and/or expand radially outward with respect to theaxial center thereof to accommodate the DiTi 302 and enhance itsfrictional attachment or “mating” of the transport arm 300 with thecoupling element 104.

A plurality of protrusions 122 extend radially outward from proximal rim125 surrounding the proximal end opening 112 of the coupling element104. The protrusions 122 are preferably substantially equal distancesapart from one another on the rim 125, and facilitate stacking and/ordocking of the coupling elements 104 (as separate components) and/or thefully assembled cleaning members 100 within a well of a multi-well trayfor use in an automated sample testing system (as described herein).

The coupling element 104 may be molded from a number of differentpolymer and heteropolymer resins, including, but not limited to,polyolefins (e.g., high density polyethylene (“HDPE”), low densitypolyethylene (“LDPE”), a mixture of HDPE and LDPE, or polypropylene),polystyrene, high impact polystyrene and polycarbonate. Although LDPE isa softer, more malleable material than HDPE, the softness of LDPEprovides greater flexibility in the distally projecting extension member105 and protuberances 106, for securably engaging the cleaning element102 within the cavity 107. Such added flexibility may also facilitatethe frictional engagement of the working end 302 of the transport arm300 within the proximal interior cavity 117 of the coupling element 104.In a presently preferred embodiment, the coupling element 104 is formedout of polypropylene (“PP”). Regardless of the type or mixture of therespective chosen materials, the cleaning element 102 and the couplingelement 104 are preferably made using a known molding process, such asby injection, compression, transfer or RTV molding. The elements 102 and104 may be molded as separate components that are later joined together,or as a single component manufactured using a known co-molding (or“over-molding”) process in which the cleaning element 102 is molded ontothe extension member 105 of the coupling member 104, so that the twocomponents are joined together in the manufacturing process.

The cleaning element 102 has a uni-body construction that may be formedusing a known injection molding process. The materials used in themolding process should be oil free and any mold-release agents usedduring the molding process are preferably limited to ones that do notleave an oily residue on the surface 114 of the cleaning element 102. Invarious embodiments, one or more cleaning elements 102 may be made outof an adhesive material, such as (without limitation) silicone, platinumcured silicone, thermoplastic polyurethane, thermoplastic elastomer,thermoplastic rubber, or a gel. A preferred adhesive material is onethat is tacky, but does not leave a residue on surfaces which itcontacts.

Alternatively or additionally, one or more cleaning elements 102 may bemade out of a material that generates a static attraction toparticulates and/or other materials that can interfere with thetransmission by the optical element of electromagnetic radiation emittedor reflected by the sample, such as (without limitation) silicon,polyvinyl chloride, polypropylene, polyethylene, polyurethane, polyesteror polystyrene. Notably, some of the foregoing materials that areadhesive also generate a static attraction to unwanted debris.

Alternatively or additionally, one or more cleaning elements 102 may bemade out of an absorbent material capable of retaining a fluid cleaningand/or sterilizing substance, and of applying the retained fluid to thesurface of the respective structure being cleaned and/or sterilized.Such absorbent materials include but are not limited to hydrophilicmaterials, and may also include hydrophobic materials such as PP andother plastics. Additional examples of absorbent materials that may beused for forming the cleaning element 102 include, without limitation,porous plastic materials in a sponge or foam form made of materials suchas PP, HDPE, LDPE, polytetrafluoroethylene (“PTFE”), polyvinylidenefluoride (“PVDF”), ethylene vinyl acetate (“EVA”), Porex® polymers,cellulose fibers (such as cotton fabric or cloth), and polymicro fibers.Exemplary fluid cleaning and/or sterilizing substances that may be usedinclude, without limitation, isopropyl alcohol, ethyl alcohol, dilutedhydrochloric acid (e.g., 20% solution), oxalic acid, diluted sodiumhydroxide (e.g., 50% solution), and diluted sodium hypochlorite (e.g.,15% solution). A preferred cleaning and/or sterilizing fluid should be acomposition that is easily removed (e.g., by reabsorption orevaporation), and should not leave a residue on the respective opticalelement after contact. Certain fluids should not be used, such as windowcleaning fluids with ammonia, gasoline, denatured alcohol, carbontetrachloride and or acetone, since such fluids may damage therespective optical element and/or sample test receptacle well. Thecleaning and/or sterilizing fluid is kept in a separate receptacle fromthe absorbent cleaning elements 102, which are at least partiallyinserted into the cleaning and/or sterilizing fluid at the time of use.Alternatively, the absorbent cleaning elements 102 may be pre-soakedwith the cleaning and/or sterilizing fluid prior to being supplied foruse.

In various embodiments, the cleaning element 102 may have differentshapes, dimensions and configurations as best suited for performing thecleaning and/or sterilizing functions of the sample testing system inwhich it is used. For example, cleaning elements 102 of selectedcleaning members 100 may be specially shaped and/or dimensioned forreaching and cleaning and/or sterilizing particular types of opticalelements, test receptacle wells, and other components of a sampletesting system in which they are used. The distal end 116 of thecleaning element 102 may be flat or curved, and preferably is at leastsomewhat compressible to avoid damaging components of the test systemduring the cleaning process.

In some embodiments, a sample testing system may be provided withmultiple types of cleaning members 100, including one or more cleaningmembers 100 having cleaning elements 102 made of a first (e.g.,adhesive) material, and one or more additional cleaning members 100having cleaning elements 102 made of a second (e.g., absorbent)material. For example, a sample test system may be provided with a oneor more cleaning members 100 having adhesive cleaning elements 102, andone or more cleaning members 100 having absorbent cleaning elements 102that retain a cleaning and/or sterilizing fluid, wherein a cleaningmember 100 having an adhesive cleaning element 102 is used to perform aninitial cleaning of one or more optical elements, and a cleaning member100 having a fluid-retaining cleaning element 102 is thereafter used toperform a secondary (i.e., finishing) cleaning of the same one or moreoptical elements.

FIGS. 4 and 5 are respective cross-sectional side elevation andcross-sectional side perspective views of the DiTi 302 of the automatedtransport arm 300 inserting an already detachably-coupled cleaningmember 100 into a test receptacle well 415 of a test receptacle holder408 positioned on a processing deck of a sample testing system(described below in greater detail), wherein the distal end surface 116of the cleaning element 102 contacts an upward axial facing end surface452 of an optical fiber 450 surrounded by a sleeve 454, positionedproximate to an open bottom portion 416 of the test receptacle well 415.By way of non-limiting example, the test receptacle holder 408 comprisesa plurality of test receptacle wells 415 (two adjacent wells 415 orshown in FIGS. 4 and 5), and the sample testing system may be providedwith a plurality of similar test receptacle holders 408, each having aplurality of test receptacle wells 415. It should be appreciated that,in alternate embodiments of sample testing systems, a test receptacleholder may have a different construct, for example, a platform forholding a microtiter plate.

The automated transport arm 300, and the DiTi 302 in particular, areconfigured to detachably couple a fully assembled cleaning member 100located in a cleaning member well of a nearby cleaning member holder,(such as cleaning member well 426 of the cleaning member storage tray424 shown in FIGS. 9-14, described below), or to otherwise firstdetachably couple a coupling element 104 located in a coupling elementholder (not shown) and thereafter join a cleaning element 102 located ina separate (e.g., environmentally sealed) cleaning element holder (alsonot shown) to the already detachably-coupled coupling element 104 tothereby have a detachably-coupled cleaning member 100. In either case,the transport arm 300 maneuvers the DiTi 302 to insert thedetachably-coupled cleaning member 100 into the test receptacle well415, as shown in FIGS. 4 and 5, such that a distal tip 116 of thecleaning element 102 is contacting (to thereby clean and/or sterilize)the axial facing distal end 452 of an optical fiber 450 positionedproximate to the open bottom end 416 of the test receptacle well 415. Itshould be appreciated that it is not necessarily required for the distaltip 116 of the cleaning element 102 to make physical contact with theaxial facing end 452 of the optical fiber 450, for example, if thecleaning element 102 comprises a material that generates a staticattraction to clean the optical fiber end 452, as described above.

It should be appreciated that optical fiber 450 can be one of aplurality of optical fibers (not shown in the Figures) employed by thesample testing system to conduct optical interrogation of samplescontained in test receptacles seated in the respective test receptaclewells 415. In particular, the optical fiber(s) 450 transmitelectromagnetic radiation (which may or may not be in the visible lightspectrum) that is emitted and/or reflected by the sample, as isexplained in detail in the above-incorporated patent applications. Itshould be appreciated that optical elements other than optical fibersmay be used for this purpose in alternate sample testing systems, and inparticular other optical elements having a protective surface, such as(without limitation) a fluorometer comprised of fixed lenses andfilters, a photomultiplier tube (“PMT”), and/or other optical elementsused in the field of biological sample testing, such as a lens, window,mirror, reflector, filter, film, and/or the like disposed between thesample and an illuminator (e.g., lasers, LEDs, tungsten, halogen,mercury arc, xenon arc, metal halide lamps) or detector (PMT, CCD, CMOS,photodiodes, photodiode array). Regardless of the type of opticalelement(s) that may be employed by a sample testing system, it iscritical that the optical pathway extending between, and including, theend surfaces of the respective optical element and test receptacle befree and clear of any debris that may interfere with the opticalinterrogation process. Thus, the cleaning members 100 of variousembodiments may be suitably modified to accommodate the cleaning and/orsterilizing alternative types of optical elements and/or test receptacleconfigurations that may be employed in various sample testing systems.

Although practice of the disclosed embodiments is not limited to thecleaning element 102 having any particular shape or dimensions, in theillustrated embodiment, the outer surface 114 of the cleaning element102 and the interior surface 413 of the test receptacle well 415 havecomplementary, generally frustoconical shapes. In this manner, thecleaning element 102 advantageously contacts to clean and/or sterilizethe interior surface 413 of the test receptacle well 415 at the sametime that the distal end 416 of the cleaning element 102 contacts toclean and/or sterilize the end surface 452 of the optical fiber 450.

FIG. 6 depicts one embodiment of a sample processing instrument deck 400of a sample testing system, in which an automated transport arm assembly(such as the below-described automated transport arm gantry 402 andassociated transport arms 410 and 418 shown in FIGS. 7 and 8) is omittedfor clarity. The sample processing instrument deck 400 includes a dozentest receptacle holders 408, each holder 408 having five test receptaclewells 415, for a total of sixty test receptacle wells 415. Theindividual receptacle holders 408 are best seen in the partialperspective view of an alternate embodiment sample processing instrumentdeck 400′ depicted in (below-described) FIG. 14. Reference is made tothe above-incorporated U.S. application Ser. No. 14/213,900, whichdiscloses additional details of an exemplary sample processinginstrument deck, and of the operation of an exemplary sample testingsystem of which the instrument deck is a part.

FIG. 7 depicts an exemplary automated transport system gantry 402,including a pair of transport arms 410 and 418 (transport arm 410 isalso shown in FIG. 8). The transport system gantry 402 can be employedin embodiments of a sample processing instrument deck, includingembodiments incorporating and using the cleaning members 100 disclosedherein (such as instrument deck 400′ of below-described FIG. 14). Whilethe depicted transport arms 410 and 418 are different in appearance fromthe automated transport arm 300 (including the DiTi interface and sleeve302/308) depicted in FIGS. 1, 4 and 5, the operation and functionalityof the transport arms 410, 418 is substantially the same as fortransport arm 300. Thus, the transport system gantry 402, includingtransport arms 410 and 418, is illustrated and described herein forpurposes of better understanding the operation of the automatedtransport arm 300 and DiTi/sleeve 302/308 depicted in theabove-described embodiments of FIGS. 1-5.

Transport arms 410 and 418 may be used for detachably coupling andtransporting objects, such as the cleaning members 100, along two axes(i.e., X and Y) in order to position the detachably-coupled objects atrespective targeted locations of a sample processing instrument deck(e.g., instrument deck 400′ of FIG. 14). In particular, the transportsystem gantry 402 can be used for detachably coupling, moving,inserting, and detaching the cleaning members 100, as described abovewith respect to the transport arm 300 of the embodiments of FIGS. 1-5.Towards this end, transport arm 410 is movable along a first X axis rail412, and transport arm 418 is movable along a second X axis rail 420.The X axis rails 412 and 420 are, in turn, both movable along a pair ofY axis rails 404 and 406. In this manner, the respective X rails 412 and420, and Y axis rails 404 and 406, collectively facilitate movement ofthe transport arms 410 and 418 in order to position the respective armsabove respective targeted objects to be detachably coupled and moved totargeted locations for positioning (e.g., inserting) and (optionally)decoupling the detachably-coupled objects. The transport arms 410 and418 are configured to move vertically (i.e., along their “Z axis”) forlowering or raising a respective detachably coupled object, e.g., forinserting a detachably-coupled cleaning member 100, relative to atargeted object underlying the respective arm. A controller (not shown)is configured to control operation of, inter alia, the transport systemgantry 402, including arms 410 and 418.

In alternate embodiments, an automated transport arm for use in thedisclosed embodiments herein may be an articulating (e.g., robotic) armthat pivots about a fixed base, although this is not necessary forpracticing the disclosed embodiments.

FIGS. 9-12 depict an exemplary cleaning member storage tray 424comprising a uni-body structure 425 that is molded out of a same orsimilar plastic material used to form the cleaning member couplingelement 104, although other suitable materials and manufacturingtechniques may be used for making the cleaning member storage tray 424.The storage tray body 425 defines a five-by-five array (i.e.,twenty-five total) inwardly recessed cleaning member wells 426. Thestorage tray body 425 has a box-like outer shape, including fourcontinuous sidewalls 430 that meet at a top surface 432 in which therespective openings of the cleaning member wells 426 are disposed. Anoutwardly protruding lip 434 substantially circumscribes a bottom endportion of the four sidewalls 430, as best seen in FIG. 10. Opposingside walls 430A and 430B of the storage tray body 425 have a pair oflaterally spaced apart slots 437 extending from respective openings 436in the bottom lip 434 of the sidewall 430A, 430B upward to an apex, theslots 437 defining flexible tabs 438A and 438B in sidewalls 430A and430B, respectively. The bottom edge of tabs 438A and 438B haverespective outwardly extending latching flanges 435A and 435B. The tabsmay be flexed into the storage tray body 425 by inwardly depressing thelatching flanges 435A and 435B into the storage tray body 425.

An exemplary cleaning member 100 is seated in a respective cleaningmember receptacle 426A in a corner of the storage tray 424. Forillustration of an alternative embodiment, there are four longitudinallyoriented linear ribs 126 formed on the interior surface 113 of thecoupling element 104 of the cleaning member of FIGS. 9-12. The linearribs 126 are spaced substantially equal distances apart from one anotheron the interior surface 113 of the cleaning member 100 of FIGS. 9-12,and are the same in dimension and features as the linear ribs 126 ofcleaning member 100 of FIGS. 1-5.

As best seen in FIGS. 10A and 10B, the cleaning member wells 426 of thestorage tray 424 include a lower portion 468 having an interior surface480 configured and dimensioned to snuggly seat the distal cleaningelement 102 of the cleaning member 100, and an upper portion 469 havinga plurality of spaced apart catch members 459 that receive and supportthe coupling element 104. The body 425 and respective storage wells 426of the cleaning member storage tray 424 are dimensioned and configuredsuch the proximal end rim 125 of the cleaning member coupling element104 is approximately co-extensive with the top surface 432 of thestorage tray 424. In this manner, the proximal open end 112 of thecleaning member coupling element 104 is readily accessible forengagement by an automated transport arm, such as the DiTi 302 oftransport arm 300 depicted in FIGS. 1, 4 and 5. For ease inillustration, no transport arm is depicted in FIGS. 9-12.

The top surface 432 of the storage tray 424 may (optionally) besubstantially environmentally sealed by a frangible sealing member (notshown) that protects and keeps the cleaning elements 102 of the cleaningmembers 100 in fresh and moist (if appropriate) condition within thewells 426, until they are ready to be used. In such embodiments, thedistal end of the DiTi 302 penetrates the respective sealing member asit is inserted into the proximal opening 112 of the cleaning membercoupling element 104. In an alternative embodiment, the cleaning memberwells 426 may be individually sealed, so that when a seal is broken toaccess and detachably couple with a respective cleaning member 100,cleaning members 100 seated in neighboring wells 426 remainsubstantially environmentally sealed. FIGS. 11A and 11B are side views,and FIG. 12 is a bottom view, respectively, of the cleaning memberstorage tray 424.

FIG. 13 depicts an exemplary cleaning member storage tray holder 422having a uni-body structure 460 molded out of a same or similar plasticmaterial used to form the cleaning member coupling element 104 and/orstorage tray 424, although other suitable materials and manufacturingtechniques may be used for making the tray holder 422. The tray holderbody 460 defines a side-by-side pair of recessed bays 462A and 462B,each bay 462A and 462B configured and dimensioned to receive arespective cleaning member storage tray 424 therein. A storage tray 424is seated in bay 462A, with its horizontal latching flanges 435A and435B extending through respective corresponding horizontal mating slots465A and 465B disposed in opposing exterior walls 461A and 461B of thetray holder body 460. The latching flange 435B and horizontal matingslot 465B are not visible in FIG. 13. However, bay 462B is also providedwith opposing horizontal mating slots 464A and 464B (both visible inFIG. 13) in the opposing walls 461A and 462B for latching a cleaningmember tray 424 in the same manner.

It should be appreciated that the cleaning member storage tray 424 canbe snap fit into the bay 462A due to the flexibility and resilience oftabs 438A and 438B of the storage tray body 425. In particular, tabs438A and 438B of the storage tray 424 may be depressed or squeezedtowards each other such that the tabs are displaced into the tray body425 to allow the storage tray 424 to be fully inserted into the bay462A. When the storage tray 424 is completely inserted into the bay462A, the latching tabs 435A and 435B are aligned with the slots 465Aand 465B, and the tabs 438A and 438B self-restore to a non-depressedconfiguration, causing the latching flanges 435A and 435B to at leastpartially extend into the respective mating slots 465A and 465B tothereby latch the storage tray 424 in bay 462A.

A teach member 466 is provided in a center area of bay 462B, and is usedby the automated transport arm (not shown) to locate items it needs tointerface with in the sample processing instrument deck (e.g.,instrument deck 400′ of FIG. 14) on which the sample receptacle trayholder 422 is mounted. The teach feature 466 in this embodiment has abox-like shape, although other shapes may be used. The automatedtransport arm will locate the feature by repeatedly driving down itsdistal tip until it force senses from the top to falling off the side.Once the transport arm locates all four sides of the teach feature 466,it interpolates the center position of the teach feature and knows thecoordinates in X, Y, Z.

Referring to FIG. 14, the cleaning member tray holder 422, including acleaning member storage tray 424 having twenty-five cleaning memberwells 426, is shown installed by bracket 469 in an exemplary sampleprocessing instrument deck 400′ of a sample testing system. Except forthe added cleaning member tray holder 422 (and cleaning member storagetray 424 mounted thereon) instrument deck 400′ is essentially identicalto instrument deck 400 of FIG. 6, including the provisioning andarrangement of a dozen test receptacle holders 408, each test receptacleholder 408 having five test receptacle wells 415 for seating sample testreceptacles containing biological samples to be optically interrogated.One or more an automated transport arms (such as the above-describedautomated transport arm 300 of the embodiment of FIGS. 1-5, or theabove-described transport arms 410 and 418 of FIG. 7) are associatedwith the instrument deck 400′ (omitted from FIG. 14 for clarity).

It should be appreciated that the cleaning member storage tray(s) 424may be manually placed into (and removed from) the storage tray holder422. In alternative embodiments, the cleaning member storage tray(s) 424may be robotically placed into (and removed from) the storage trayholder 422 by the respective automated transport arm employed fortransporting the cleaning members 100. In the latter case, amodification may be made to/in the top surface of the tray to provide acoupling element for the automated transport arm, such as by convertingthe center-most cleaning member receptacle 426 into a recess configuredfor detachably coupling with the automated arm. The instrument deck 400′preferably also includes a waste output or other designated “used”cleaning member holder (not shown), configured to at least temporarilyhold used cleaning members 100. Alternatively, the used cleaning members100 can be returned to the same or a different cleaning memberreceptacle well 426 from which they were originally taken.

In accordance with the disclosed embodiments, a controller (not shown)controls operation of an automated transport arm associated with theinstrument deck 400′ (not shown in FIG. 14) for causing the automatedtransport arm to detachably couple with a respective cleaning member 100(not shown in FIG. 14) held in a cleaning member receptacle 426 of thestorage try 424, and to move the respective detachably-coupled cleaningmember 100 into a position proximate to and/or contacting an opticalelement (e.g., the distal end of an optical fiber such as shown in FIGS.4 and 5) underlying an open bottom end of one of the test receptaclewells 415 based upon one or both of a (i) predetermined cleaningschedule, and (ii) sensed presence of particulates and/or othermaterials disposed on or over the optical element. The controller mayfurther cause the automated transport arm to deposit respectivedecoupled cleaning member 100 into a system waste output or a designatedused cleaning member holder.

Although particular embodiments have been shown and described herein, itwill be understood by those skilled in the art that they are notintended to limit the disclosure, and it will be obvious to thoseskilled in the art that various changes and modifications may be made(e.g., the dimensions of various parts) without departing from the scopeof the disclosure, which is to be defined only by the following claimsand their equivalents. The specification and drawings are, accordingly,to be regarded in an illustrative rather than restrictive sense.

The invention claimed is:
 1. A method of operating a sample testingsystem, the system comprising a test receptacle support structure and anoptical element positioned for transmitting electromagnetic radiationemitted or reflected by a sample disposed in a test receptacle supportedby the test receptacle support structure, the method comprising using anautomated transport arm to: detachably couple a cleaning member to aworking end of the transport arm, wherein the cleaning member comprisesa proximal coupling element and a distal cleaning element; move thedetachably-coupled cleaning member into a position proximate to and/orcontacting the optical element, such that the cleaning element therebycleans and/or sterilizes the optical element; and decouple the cleaningmember from the working end of the transport arm.
 2. The method of claim1, wherein the system comprises a cleaning member holder having aplurality of cleaning member receptacles, wherein the cleaning member isone of a plurality of cleaning members held in respective cleaningmember receptacles of the cleaning member holder, and wherein theautomated transport arm detachably couples the cleaning member while thecleaning member is held in the respective cleaning member receptacle. 3.The method of claim 1, wherein the automated arm detachably couples thecleaning member to the working end portion of the transport arm by:detachably coupling a proximal end portion of the coupling element tothe working end of the transport arm, and inserting a distal endconnector of the coupling element into a recessed proximal portion ofthe cleaning element to thereby attach the cleaning element to thecoupling element.
 4. The method of claim 3, wherein the distal endconnector of the coupling element forms an interference fit with theproximal recessed portion of the cleaning element.
 5. The method ofclaim 3, wherein the distal end connector of the coupling element formsa frictional fit with the proximal recessed portion of the cleaningelement.
 6. The method of claim 3, wherein the system comprises acleaning element holder having a plurality of cleaning elementreceptacles, wherein the cleaning element is one of a plurality ofcleaning elements held in respective cleaning element receptacles of thecleaning element holder.
 7. The method of claim 6, wherein the cleaningelement is substantially environmentally sealed in the respectivecleaning element receptacle by a frangible sealing member that ispierced when the distal end connector of the coupling element isinserted into the recessed proximal portion of the cleaning element. 8.The method of claim 6, wherein the automated transport arm inserts thedistal end connector of the coupling element into the recessed proximalportion of the cleaning element while the cleaning element is held inthe respective cleaning element receptacle.
 9. The method of claim 1,further comprising using the automated transport arm to move thedetachably-coupled cleaning member into a position such that thecleaning element is inserted into a test receptacle well of the testreceptacle support structure, wherein the cleaning element isdimensioned such that an outer surface of the cleaning element conformsto an interior surface of the test receptacle well.
 10. The method ofclaim 9, wherein the cleaning element cleans, decontaminates and/orsterilizes the interior surface of the test receptacle well wheninserted therein.
 11. The method of claim 9, wherein the test receptaclewell has an open bottom, and the optical element comprising an opticalfiber having an end positioned proximate to the open bottom of the testreceptacle well, and wherein the cleaning element cleans, decontaminatesand/or sterilizes the end of the optical fiber when inserted into thetest receptacle well.
 12. The method of claim 9, wherein thedetachably-coupled cleaning member comprises a first cleaning member,and wherein the cleaning element of the first cleaning member comprisesa first cleaning element, the method further comprising, afterdecoupling the first cleaning member from the working end of theautomated transport arm, using the automated transport arm to:detachably couple a second cleaning member to the working end of theautomated transport arm, the second cleaning member comprising a secondcleaning element; and move the detachably-coupled second cleaning memberinto a position such that the second cleaning element is inserted intothe same test receptacle well of the test receptacle support structure.13. The method of claim 12, wherein the first cleaning element is madeof a different material than the second cleaning element.
 14. The methodof claim 1, wherein the cleaning element comprises an adhesive material.15. The method of claim 1, wherein the cleaning element comprises amaterial that generates a static attraction to particulates and/or othermaterials that can interfere with the transmission by the opticalelement of electromagnetic radiation emitted or reflected by the sample.16. The method of claim 1, wherein the cleaning element comprises anabsorbent material capable of retaining a fluid substance.
 17. Themethod of claim 1, wherein the system comprises a controller thatcontrols operation of the automated transport arm for causing theautomated transport arm to detachably couple with a respective cleaningmember, and to move the respective detachably-coupled cleaning memberinto a position proximate to and/or contacting the optical element basedupon one or both of a (i) predetermined cleaning schedule, and (ii)sensed presence of particulates and/or other materials disposed on orover the optical element.
 18. The method of claim 17, wherein thecontroller causes the automated transport arm to deposit respectivedecoupled cleaning members into a system waste output or a designatedused cleaning member holder.